Correlation between gene mutation status and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1BZ64S2
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 28 genes and 8 molecular subtypes across 168 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

  • SETD2 mutation correlated to 'METHLYATION_CNMF'.

  • MET mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 28 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 2 significant findings detected.

Clinical
Features
CN
CNMF
METHLYATION
CNMF
MRNASEQ
CNMF
MRNASEQ
CHIERARCHICAL
MIRSEQ
CNMF
MIRSEQ
CHIERARCHICAL
MIRSEQ
MATURE
CNMF
MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
SETD2 15 (9%) 153 0.105
(1.00)
0.00103
(0.23)
0.0715
(1.00)
0.226
(1.00)
0.888
(1.00)
0.718
(1.00)
0.943
(1.00)
0.091
(1.00)
MET 15 (9%) 153 0.696
(1.00)
0.072
(1.00)
0.00056
(0.125)
0.0113
(1.00)
0.745
(1.00)
0.633
(1.00)
0.747
(1.00)
0.069
(1.00)
HNRNPM 11 (7%) 157 1
(1.00)
0.382
(1.00)
0.594
(1.00)
0.497
(1.00)
0.579
(1.00)
0.541
(1.00)
0.924
(1.00)
0.411
(1.00)
NF2 12 (7%) 156 0.0695
(1.00)
0.0148
(1.00)
0.034
(1.00)
0.932
(1.00)
0.933
(1.00)
0.676
(1.00)
1
(1.00)
0.697
(1.00)
NEFH 10 (6%) 158 0.238
(1.00)
0.911
(1.00)
0.115
(1.00)
0.227
(1.00)
0.0128
(1.00)
0.00291
(0.646)
0.00303
(0.67)
0.0982
(1.00)
TDG 5 (3%) 163 0.324
(1.00)
0.277
(1.00)
0.866
(1.00)
0.325
(1.00)
0.0766
(1.00)
0.584
(1.00)
0.16
(1.00)
0.683
(1.00)
ZNF598 13 (8%) 155 0.194
(1.00)
0.444
(1.00)
0.112
(1.00)
0.62
(1.00)
0.179
(1.00)
0.145
(1.00)
0.441
(1.00)
0.00565
(1.00)
SKI 6 (4%) 162 0.86
(1.00)
0.0624
(1.00)
0.162
(1.00)
0.876
(1.00)
0.775
(1.00)
1
(1.00)
0.879
(1.00)
0.665
(1.00)
CSGALNACT2 7 (4%) 161 0.0647
(1.00)
0.295
(1.00)
0.505
(1.00)
0.889
(1.00)
0.0813
(1.00)
0.764
(1.00)
0.207
(1.00)
0.979
(1.00)
MUC5B 18 (11%) 150 0.881
(1.00)
0.849
(1.00)
0.746
(1.00)
0.606
(1.00)
0.492
(1.00)
0.186
(1.00)
0.155
(1.00)
0.651
(1.00)
KDM6A 9 (5%) 159 0.449
(1.00)
0.831
(1.00)
0.108
(1.00)
0.39
(1.00)
0.689
(1.00)
0.732
(1.00)
0.258
(1.00)
0.208
(1.00)
ZNF814 8 (5%) 160 0.46
(1.00)
0.483
(1.00)
0.713
(1.00)
0.314
(1.00)
0.597
(1.00)
0.553
(1.00)
0.6
(1.00)
0.662
(1.00)
OR2L8 4 (2%) 164 0.458
(1.00)
0.301
(1.00)
0.481
(1.00)
0.108
(1.00)
0.322
(1.00)
0.313
(1.00)
0.2
(1.00)
0.704
(1.00)
MYH6 8 (5%) 160 0.297
(1.00)
0.294
(1.00)
0.409
(1.00)
0.599
(1.00)
0.905
(1.00)
0.235
(1.00)
0.823
(1.00)
0.313
(1.00)
UNC13A 9 (5%) 159 0.0753
(1.00)
0.834
(1.00)
0.186
(1.00)
0.833
(1.00)
0.913
(1.00)
0.483
(1.00)
1
(1.00)
0.525
(1.00)
MED16 4 (2%) 164 0.0867
(1.00)
0.0965
(1.00)
0.638
(1.00)
0.198
(1.00)
1
(1.00)
0.315
(1.00)
1
(1.00)
0.29
(1.00)
GLUD2 11 (7%) 157 1
(1.00)
0.924
(1.00)
0.464
(1.00)
0.127
(1.00)
0.28
(1.00)
0.448
(1.00)
0.0432
(1.00)
0.728
(1.00)
BMS1 13 (8%) 155 0.784
(1.00)
0.672
(1.00)
0.427
(1.00)
0.716
(1.00)
0.936
(1.00)
0.052
(1.00)
0.633
(1.00)
0.0989
(1.00)
FUS 3 (2%) 165 1
(1.00)
0.262
(1.00)
0.44
(1.00)
0.778
(1.00)
0.64
(1.00)
1
(1.00)
0.633
(1.00)
0.839
(1.00)
TP53 7 (4%) 161 0.201
(1.00)
0.0507
(1.00)
0.353
(1.00)
0.178
(1.00)
0.707
(1.00)
0.291
(1.00)
0.792
(1.00)
0.161
(1.00)
ACADL 4 (2%) 164 0.35
(1.00)
0.48
(1.00)
1
(1.00)
0.463
(1.00)
0.0181
(1.00)
0.394
(1.00)
0.146
(1.00)
0.352
(1.00)
AHNAK2 10 (6%) 158 0.435
(1.00)
0.317
(1.00)
0.0217
(1.00)
0.249
(1.00)
0.229
(1.00)
0.104
(1.00)
0.715
(1.00)
0.0327
(1.00)
SMARCB1 5 (3%) 163 1
(1.00)
0.0606
(1.00)
0.316
(1.00)
0.322
(1.00)
0.012
(1.00)
0.493
(1.00)
0.0122
(1.00)
0.918
(1.00)
TEKT1 4 (2%) 164 0.607
(1.00)
0.686
(1.00)
0.906
(1.00)
0.831
(1.00)
0.463
(1.00)
0.514
(1.00)
1
(1.00)
0.362
(1.00)
MKL1 9 (5%) 159 0.0773
(1.00)
0.717
(1.00)
0.142
(1.00)
0.472
(1.00)
0.913
(1.00)
0.278
(1.00)
1
(1.00)
0.996
(1.00)
MYH7 6 (4%) 162 0.606
(1.00)
1
(1.00)
0.376
(1.00)
0.383
(1.00)
0.774
(1.00)
0.0372
(1.00)
0.88
(1.00)
0.251
(1.00)
MAP4K3 5 (3%) 163 0.827
(1.00)
0.379
(1.00)
0.274
(1.00)
0.228
(1.00)
0.133
(1.00)
0.203
(1.00)
0.104
(1.00)
0.759
(1.00)
NEK2 3 (2%) 165 1
(1.00)
0.784
(1.00)
0.515
(1.00)
0.196
(1.00)
0.296
(1.00)
0.182
(1.00)
0.273
(1.00)
0.696
(1.00)
'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
HNRNPM MUTATED 4 6 1
HNRNPM WILD-TYPE 57 79 21
'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
HNRNPM MUTATED 5 3 3
HNRNPM WILD-TYPE 37 44 61
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
HNRNPM MUTATED 1 4 3 3
HNRNPM WILD-TYPE 36 57 41 23
'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
HNRNPM MUTATED 3 3 5
HNRNPM WILD-TYPE 61 51 45
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.579 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
HNRNPM MUTATED 2 4 5
HNRNPM WILD-TYPE 54 46 57
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
HNRNPM MUTATED 4 3 4
HNRNPM WILD-TYPE 77 27 53
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
HNRNPM MUTATED 3 3 5
HNRNPM WILD-TYPE 57 43 57
'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
HNRNPM MUTATED 2 0 1 1 4 3 0
HNRNPM WILD-TYPE 18 27 22 19 27 28 16
'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0695 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
NF2 MUTATED 1 9 2
NF2 WILD-TYPE 60 76 20
'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0148 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
NF2 MUTATED 0 7 4
NF2 WILD-TYPE 42 40 60

Figure S1.  Get High-res Image Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
NF2 MUTATED 0 7 5 0
NF2 WILD-TYPE 37 54 39 26

Figure S2.  Get High-res Image Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
NF2 MUTATED 4 4 4
NF2 WILD-TYPE 60 50 46
'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
NF2 MUTATED 4 3 5
NF2 WILD-TYPE 52 47 57
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
NF2 MUTATED 6 1 5
NF2 WILD-TYPE 75 29 52
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
NF2 MUTATED 4 3 5
NF2 WILD-TYPE 56 43 57
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.697 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
NF2 MUTATED 1 2 2 1 1 2 3
NF2 WILD-TYPE 19 25 21 19 30 29 13
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
NEFH MUTATED 3 4 3
NEFH WILD-TYPE 58 81 19
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S18.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
NEFH MUTATED 3 2 4
NEFH WILD-TYPE 39 45 60
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
NEFH MUTATED 5 2 3 0
NEFH WILD-TYPE 32 59 41 26
'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
NEFH MUTATED 6 1 3
NEFH WILD-TYPE 58 53 47
'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
NEFH MUTATED 6 4 0
NEFH WILD-TYPE 50 46 62

Figure S3.  Get High-res Image Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00291 (Fisher's exact test), Q value = 0.65

Table S22.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
NEFH MUTATED 10 0 0
NEFH WILD-TYPE 71 30 57

Figure S4.  Get High-res Image Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00303 (Fisher's exact test), Q value = 0.67

Table S23.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
NEFH MUTATED 8 2 0
NEFH WILD-TYPE 52 44 62

Figure S5.  Get High-res Image Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0982 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
NEFH MUTATED 2 2 4 0 0 2 0
NEFH WILD-TYPE 18 25 19 20 31 29 16
'TDG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S25.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
TDG MUTATED 3 1 1
TDG WILD-TYPE 58 84 21
'TDG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S26.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
TDG MUTATED 0 3 2
TDG WILD-TYPE 42 44 62
'TDG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
TDG MUTATED 1 3 1 0
TDG WILD-TYPE 36 58 43 26
'TDG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.325 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
TDG MUTATED 3 0 2
TDG WILD-TYPE 61 54 48
'TDG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
TDG MUTATED 4 0 1
TDG WILD-TYPE 52 50 61
'TDG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
TDG MUTATED 4 0 1
TDG WILD-TYPE 77 30 56
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
TDG MUTATED 4 0 1
TDG WILD-TYPE 56 46 61
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'TDG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
TDG MUTATED 1 2 1 0 1 0 0
TDG WILD-TYPE 19 25 22 20 30 31 16
'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
ZNF598 MUTATED 2 8 3
ZNF598 WILD-TYPE 59 77 19
'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S34.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
ZNF598 MUTATED 4 5 3
ZNF598 WILD-TYPE 38 42 61
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
ZNF598 MUTATED 1 5 2 5
ZNF598 WILD-TYPE 36 56 42 21
'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S36.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
ZNF598 MUTATED 4 6 3
ZNF598 WILD-TYPE 60 48 47
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
ZNF598 MUTATED 2 3 8
ZNF598 WILD-TYPE 54 47 54
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
ZNF598 MUTATED 3 3 7
ZNF598 WILD-TYPE 78 27 50
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
ZNF598 MUTATED 3 3 7
ZNF598 WILD-TYPE 57 43 55
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00565 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
ZNF598 MUTATED 0 3 0 1 7 0 2
ZNF598 WILD-TYPE 20 24 23 19 24 31 14

Figure S6.  Get High-res Image Gene #5: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S41.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
SKI MUTATED 2 4 0
SKI WILD-TYPE 59 81 22
'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0624 (Fisher's exact test), Q value = 1

Table S42.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
SKI MUTATED 4 0 2
SKI WILD-TYPE 38 47 62
'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S43.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
SKI MUTATED 1 1 1 3
SKI WILD-TYPE 36 60 43 23
'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S44.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
SKI MUTATED 3 2 1
SKI WILD-TYPE 61 52 49
'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
SKI MUTATED 3 1 2
SKI WILD-TYPE 53 49 60
'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
SKI MUTATED 3 1 2
SKI WILD-TYPE 78 29 55
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
SKI MUTATED 2 1 3
SKI WILD-TYPE 58 45 59
'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
SKI MUTATED 0 2 0 0 2 2 0
SKI WILD-TYPE 20 25 23 20 29 29 16
'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0647 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
CSGALNACT2 MUTATED 1 3 3
CSGALNACT2 WILD-TYPE 60 82 19
'CSGALNACT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 1

Table S50.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
CSGALNACT2 MUTATED 4 1 2
CSGALNACT2 WILD-TYPE 38 46 62
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
CSGALNACT2 MUTATED 0 4 2 1
CSGALNACT2 WILD-TYPE 37 57 42 25
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S52.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
CSGALNACT2 MUTATED 2 3 2
CSGALNACT2 WILD-TYPE 62 51 48
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0813 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
CSGALNACT2 MUTATED 1 5 1
CSGALNACT2 WILD-TYPE 55 45 61
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
CSGALNACT2 MUTATED 3 2 2
CSGALNACT2 WILD-TYPE 78 28 55
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
CSGALNACT2 MUTATED 2 4 1
CSGALNACT2 WILD-TYPE 58 42 61
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.979 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
CSGALNACT2 MUTATED 0 1 1 1 2 1 1
CSGALNACT2 WILD-TYPE 20 26 22 19 29 30 15
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S57.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
SETD2 MUTATED 2 10 3
SETD2 WILD-TYPE 59 75 19
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.23

Table S58.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
SETD2 MUTATED 1 11 3
SETD2 WILD-TYPE 41 36 61

Figure S7.  Get High-res Image Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0715 (Fisher's exact test), Q value = 1

Table S59.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
SETD2 MUTATED 2 10 3 0
SETD2 WILD-TYPE 35 51 41 26
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 1

Table S60.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
SETD2 MUTATED 9 3 3
SETD2 WILD-TYPE 55 51 47
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S61.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
SETD2 MUTATED 6 4 5
SETD2 WILD-TYPE 50 46 57
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
SETD2 MUTATED 9 2 4
SETD2 WILD-TYPE 72 28 53
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.943 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
SETD2 MUTATED 6 4 5
SETD2 WILD-TYPE 54 42 57
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.091 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
SETD2 MUTATED 1 6 0 0 3 4 1
SETD2 WILD-TYPE 19 21 23 20 28 27 15
'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MET MUTATED 7 7 1
MET WILD-TYPE 54 78 21
'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 1

Table S66.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MET MUTATED 3 1 9
MET WILD-TYPE 39 46 55
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00056 (Fisher's exact test), Q value = 0.13

Table S67.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MET MUTATED 1 1 6 7
MET WILD-TYPE 36 60 38 19

Figure S8.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MET MUTATED 4 10 1
MET WILD-TYPE 60 44 49

Figure S9.  Get High-res Image Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S69.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MET MUTATED 6 3 6
MET WILD-TYPE 50 47 56
'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MET MUTATED 6 2 7
MET WILD-TYPE 75 28 50
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S71.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MET MUTATED 5 3 7
MET WILD-TYPE 55 43 55
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.069 (Fisher's exact test), Q value = 1

Table S72.  Gene #9: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MET MUTATED 4 1 1 5 2 2 0
MET WILD-TYPE 16 26 22 15 29 29 16
'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.881 (Fisher's exact test), Q value = 1

Table S73.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MUC5B MUTATED 6 9 3
MUC5B WILD-TYPE 55 76 19
'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S74.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MUC5B MUTATED 5 6 6
MUC5B WILD-TYPE 37 41 58
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S75.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MUC5B MUTATED 3 9 4 2
MUC5B WILD-TYPE 34 52 40 24
'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S76.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MUC5B MUTATED 9 5 4
MUC5B WILD-TYPE 55 49 46
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 1

Table S77.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MUC5B MUTATED 5 4 9
MUC5B WILD-TYPE 51 46 53
'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S78.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MUC5B MUTATED 10 5 3
MUC5B WILD-TYPE 71 25 54
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 1

Table S79.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MUC5B MUTATED 6 2 10
MUC5B WILD-TYPE 54 44 52
'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S80.  Gene #10: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MUC5B MUTATED 2 6 1 2 3 3 1
MUC5B WILD-TYPE 18 21 22 18 28 28 15
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S81.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
KDM6A MUTATED 5 3 1
KDM6A WILD-TYPE 56 82 21
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S82.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
KDM6A MUTATED 3 3 3
KDM6A WILD-TYPE 39 44 61
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S83.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
KDM6A MUTATED 5 2 2 0
KDM6A WILD-TYPE 32 59 42 26
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 1

Table S84.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
KDM6A MUTATED 5 1 3
KDM6A WILD-TYPE 59 53 47
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S85.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
KDM6A MUTATED 4 3 2
KDM6A WILD-TYPE 52 47 60
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S86.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
KDM6A MUTATED 5 2 2
KDM6A WILD-TYPE 76 28 55
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 1

Table S87.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
KDM6A MUTATED 5 3 1
KDM6A WILD-TYPE 55 43 61
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 1

Table S88.  Gene #11: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
KDM6A MUTATED 3 1 1 0 0 3 1
KDM6A WILD-TYPE 17 26 22 20 31 28 15
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 1

Table S89.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
ZNF814 MUTATED 3 3 2
ZNF814 WILD-TYPE 58 82 20
'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S90.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
ZNF814 MUTATED 1 4 3
ZNF814 WILD-TYPE 41 43 61
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S91.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
ZNF814 MUTATED 2 4 2 0
ZNF814 WILD-TYPE 35 57 42 26
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 1

Table S92.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
ZNF814 MUTATED 5 1 2
ZNF814 WILD-TYPE 59 53 48
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S93.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
ZNF814 MUTATED 3 1 4
ZNF814 WILD-TYPE 53 49 58
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S94.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
ZNF814 MUTATED 5 0 3
ZNF814 WILD-TYPE 76 30 54
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S95.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
ZNF814 MUTATED 3 1 4
ZNF814 WILD-TYPE 57 45 58
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S96.  Gene #12: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
ZNF814 MUTATED 0 3 1 0 2 1 1
ZNF814 WILD-TYPE 20 24 22 20 29 30 15
'OR2L8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S97.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
OR2L8 MUTATED 2 1 1
OR2L8 WILD-TYPE 59 84 21
'OR2L8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 1

Table S98.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
OR2L8 MUTATED 2 0 2
OR2L8 WILD-TYPE 40 47 62
'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S99.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
OR2L8 MUTATED 0 1 2 1
OR2L8 WILD-TYPE 37 60 42 25
'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S100.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
OR2L8 MUTATED 0 3 1
OR2L8 WILD-TYPE 64 51 49
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S101.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
OR2L8 MUTATED 0 1 3
OR2L8 WILD-TYPE 56 49 59
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S102.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
OR2L8 MUTATED 1 0 3
OR2L8 WILD-TYPE 80 30 54
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 1

Table S103.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
OR2L8 MUTATED 0 1 3
OR2L8 WILD-TYPE 60 45 59
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S104.  Gene #13: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
OR2L8 MUTATED 0 0 0 1 2 1 0
OR2L8 WILD-TYPE 20 27 23 19 29 30 16
'MYH6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 1

Table S105.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MYH6 MUTATED 1 6 1
MYH6 WILD-TYPE 60 79 21
'MYH6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 1

Table S106.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MYH6 MUTATED 4 1 3
MYH6 WILD-TYPE 38 46 61
'MYH6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S107.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MYH6 MUTATED 1 2 2 3
MYH6 WILD-TYPE 36 59 42 23
'MYH6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S108.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MYH6 MUTATED 2 4 2
MYH6 WILD-TYPE 62 50 48
'MYH6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S109.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MYH6 MUTATED 2 3 3
MYH6 WILD-TYPE 54 47 59
'MYH6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 1

Table S110.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MYH6 MUTATED 2 1 5
MYH6 WILD-TYPE 79 29 52
'MYH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S111.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MYH6 MUTATED 2 3 3
MYH6 WILD-TYPE 58 43 59
'MYH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S112.  Gene #14: 'MYH6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MYH6 MUTATED 2 0 0 1 2 1 2
MYH6 WILD-TYPE 18 27 23 19 29 30 14
'UNC13A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0753 (Fisher's exact test), Q value = 1

Table S113.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
UNC13A MUTATED 1 8 0
UNC13A WILD-TYPE 60 77 22
'UNC13A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S114.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
UNC13A MUTATED 3 3 3
UNC13A WILD-TYPE 39 44 61
'UNC13A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 1

Table S115.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
UNC13A MUTATED 0 4 2 3
UNC13A WILD-TYPE 37 57 42 23
'UNC13A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S116.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
UNC13A MUTATED 4 2 3
UNC13A WILD-TYPE 60 52 47
'UNC13A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S117.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
UNC13A MUTATED 3 2 4
UNC13A WILD-TYPE 53 48 58
'UNC13A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S118.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
UNC13A MUTATED 3 1 5
UNC13A WILD-TYPE 78 29 52
'UNC13A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S119.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
UNC13A MUTATED 3 2 4
UNC13A WILD-TYPE 57 44 58
'UNC13A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.525 (Fisher's exact test), Q value = 1

Table S120.  Gene #15: 'UNC13A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
UNC13A MUTATED 1 2 0 1 4 1 0
UNC13A WILD-TYPE 19 25 23 19 27 30 16
'MED16 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0867 (Fisher's exact test), Q value = 1

Table S121.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MED16 MUTATED 0 2 2
MED16 WILD-TYPE 61 83 20
'MED16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0965 (Fisher's exact test), Q value = 1

Table S122.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MED16 MUTATED 1 3 0
MED16 WILD-TYPE 41 44 64
'MED16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S123.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MED16 MUTATED 1 2 0 1
MED16 WILD-TYPE 36 59 44 25
'MED16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 1

Table S124.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MED16 MUTATED 1 3 0
MED16 WILD-TYPE 63 51 50
'MED16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S125.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MED16 MUTATED 1 1 2
MED16 WILD-TYPE 55 49 60
'MED16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.315 (Fisher's exact test), Q value = 1

Table S126.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MED16 MUTATED 1 0 3
MED16 WILD-TYPE 80 30 54
'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S127.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MED16 MUTATED 1 1 2
MED16 WILD-TYPE 59 45 60
'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S128.  Gene #16: 'MED16 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MED16 MUTATED 1 0 0 0 2 0 1
MED16 WILD-TYPE 19 27 23 20 29 31 15
'GLUD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S129.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
GLUD2 MUTATED 4 6 1
GLUD2 WILD-TYPE 57 79 21
'GLUD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S130.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
GLUD2 MUTATED 3 4 4
GLUD2 WILD-TYPE 39 43 60
'GLUD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S131.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
GLUD2 MUTATED 4 4 1 2
GLUD2 WILD-TYPE 33 57 43 24
'GLUD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S132.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
GLUD2 MUTATED 7 1 3
GLUD2 WILD-TYPE 57 53 47
'GLUD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S133.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
GLUD2 MUTATED 6 3 2
GLUD2 WILD-TYPE 50 47 60
'GLUD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.448 (Fisher's exact test), Q value = 1

Table S134.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
GLUD2 MUTATED 6 3 2
GLUD2 WILD-TYPE 75 27 55
'GLUD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0432 (Fisher's exact test), Q value = 1

Table S135.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
GLUD2 MUTATED 8 1 2
GLUD2 WILD-TYPE 52 45 60

Figure S10.  Get High-res Image Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'GLUD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S136.  Gene #17: 'GLUD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
GLUD2 MUTATED 2 3 2 0 2 2 0
GLUD2 WILD-TYPE 18 24 21 20 29 29 16
'BMS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S137.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
BMS1 MUTATED 4 8 1
BMS1 WILD-TYPE 57 77 21
'BMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 1

Table S138.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
BMS1 MUTATED 3 2 6
BMS1 WILD-TYPE 39 45 58
'BMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 1

Table S139.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
BMS1 MUTATED 3 3 3 4
BMS1 WILD-TYPE 34 58 41 22
'BMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S140.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
BMS1 MUTATED 4 4 5
BMS1 WILD-TYPE 60 50 45
'BMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S141.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
BMS1 MUTATED 5 4 4
BMS1 WILD-TYPE 51 46 58
'BMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.052 (Fisher's exact test), Q value = 1

Table S142.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
BMS1 MUTATED 10 2 1
BMS1 WILD-TYPE 71 28 56
'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S143.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
BMS1 MUTATED 3 4 6
BMS1 WILD-TYPE 57 42 56
'BMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0989 (Fisher's exact test), Q value = 1

Table S144.  Gene #18: 'BMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
BMS1 MUTATED 1 0 4 0 2 5 1
BMS1 WILD-TYPE 19 27 19 20 29 26 15
'FUS MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S145.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
FUS MUTATED 1 2 0
FUS WILD-TYPE 60 83 22
'FUS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S146.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
FUS MUTATED 1 2 0
FUS WILD-TYPE 41 45 64
'FUS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S147.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
FUS MUTATED 0 2 0 1
FUS WILD-TYPE 37 59 44 25
'FUS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S148.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
FUS MUTATED 2 1 0
FUS WILD-TYPE 62 53 50
'FUS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 1

Table S149.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
FUS MUTATED 2 0 1
FUS WILD-TYPE 54 50 61
'FUS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S150.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
FUS MUTATED 2 0 1
FUS WILD-TYPE 79 30 56
'FUS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S151.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
FUS MUTATED 2 0 1
FUS WILD-TYPE 58 46 61
'FUS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S152.  Gene #19: 'FUS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
FUS MUTATED 1 1 0 0 1 0 0
FUS WILD-TYPE 19 26 23 20 30 31 16
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 1

Table S153.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
TP53 MUTATED 1 6 0
TP53 WILD-TYPE 60 79 22
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0507 (Fisher's exact test), Q value = 1

Table S154.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
TP53 MUTATED 3 3 0
TP53 WILD-TYPE 39 44 64
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 1

Table S155.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
TP53 MUTATED 2 4 0 1
TP53 WILD-TYPE 35 57 44 25
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S156.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
TP53 MUTATED 3 4 0
TP53 WILD-TYPE 61 50 50
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 1

Table S157.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
TP53 MUTATED 3 1 3
TP53 WILD-TYPE 53 49 59
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 1

Table S158.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
TP53 MUTATED 3 0 4
TP53 WILD-TYPE 78 30 53
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S159.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
TP53 MUTATED 3 1 3
TP53 WILD-TYPE 57 45 59
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S160.  Gene #20: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
TP53 MUTATED 1 1 0 0 1 1 3
TP53 WILD-TYPE 19 26 23 20 30 30 13
'ACADL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 1

Table S161.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
ACADL MUTATED 3 1 0
ACADL WILD-TYPE 58 84 22
'ACADL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 1

Table S162.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
ACADL MUTATED 0 2 1
ACADL WILD-TYPE 42 45 63
'ACADL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S163.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
ACADL MUTATED 1 2 1 0
ACADL WILD-TYPE 36 59 43 26
'ACADL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S164.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
ACADL MUTATED 2 0 2
ACADL WILD-TYPE 62 54 48
'ACADL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0181 (Fisher's exact test), Q value = 1

Table S165.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
ACADL MUTATED 4 0 0
ACADL WILD-TYPE 52 50 62

Figure S11.  Get High-res Image Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'ACADL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 1

Table S166.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
ACADL MUTATED 3 1 0
ACADL WILD-TYPE 78 29 57
'ACADL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S167.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
ACADL MUTATED 3 1 0
ACADL WILD-TYPE 57 45 62
'ACADL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S168.  Gene #21: 'ACADL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
ACADL MUTATED 0 2 0 0 0 2 0
ACADL WILD-TYPE 20 25 23 20 31 29 16
'AHNAK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S169.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
AHNAK2 MUTATED 2 6 2
AHNAK2 WILD-TYPE 59 79 20
'AHNAK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S170.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
AHNAK2 MUTATED 4 1 4
AHNAK2 WILD-TYPE 38 46 60
'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 1

Table S171.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
AHNAK2 MUTATED 2 1 2 5
AHNAK2 WILD-TYPE 35 60 42 21

Figure S12.  Get High-res Image Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 1

Table S172.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
AHNAK2 MUTATED 6 3 1
AHNAK2 WILD-TYPE 58 51 49
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S173.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
AHNAK2 MUTATED 6 2 2
AHNAK2 WILD-TYPE 50 48 60
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 1

Table S174.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
AHNAK2 MUTATED 8 0 2
AHNAK2 WILD-TYPE 73 30 55
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S175.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
AHNAK2 MUTATED 5 2 3
AHNAK2 WILD-TYPE 55 44 59
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0327 (Fisher's exact test), Q value = 1

Table S176.  Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
AHNAK2 MUTATED 4 1 0 2 0 3 0
AHNAK2 WILD-TYPE 16 26 23 18 31 28 16

Figure S13.  Get High-res Image Gene #22: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SMARCB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S177.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
SMARCB1 MUTATED 2 3 0
SMARCB1 WILD-TYPE 59 82 22
'SMARCB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0606 (Fisher's exact test), Q value = 1

Table S178.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
SMARCB1 MUTATED 0 4 1
SMARCB1 WILD-TYPE 42 43 63
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 1

Table S179.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
SMARCB1 MUTATED 0 4 1 0
SMARCB1 WILD-TYPE 37 57 43 26
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S180.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
SMARCB1 MUTATED 3 0 2
SMARCB1 WILD-TYPE 61 54 48
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 1

Table S181.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
SMARCB1 MUTATED 0 0 5
SMARCB1 WILD-TYPE 56 50 57

Figure S14.  Get High-res Image Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S182.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
SMARCB1 MUTATED 2 0 3
SMARCB1 WILD-TYPE 79 30 54
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 1

Table S183.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
SMARCB1 MUTATED 0 0 5
SMARCB1 WILD-TYPE 60 46 57

Figure S15.  Get High-res Image Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S184.  Gene #23: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
SMARCB1 MUTATED 0 1 0 1 2 1 0
SMARCB1 WILD-TYPE 20 26 23 19 29 30 16
'TEKT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S185.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
TEKT1 MUTATED 1 2 1
TEKT1 WILD-TYPE 60 83 21
'TEKT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S186.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
TEKT1 MUTATED 2 1 1
TEKT1 WILD-TYPE 40 46 63
'TEKT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S187.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
TEKT1 MUTATED 1 1 1 1
TEKT1 WILD-TYPE 36 60 43 25
'TEKT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S188.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
TEKT1 MUTATED 1 2 1
TEKT1 WILD-TYPE 63 52 49
'TEKT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S189.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
TEKT1 MUTATED 0 2 2
TEKT1 WILD-TYPE 56 48 60
'TEKT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S190.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
TEKT1 MUTATED 1 1 2
TEKT1 WILD-TYPE 80 29 55
'TEKT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S191.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
TEKT1 MUTATED 1 1 2
TEKT1 WILD-TYPE 59 45 60
'TEKT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S192.  Gene #24: 'TEKT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
TEKT1 MUTATED 0 0 1 0 2 0 1
TEKT1 WILD-TYPE 20 27 22 20 29 31 15
'MKL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0773 (Fisher's exact test), Q value = 1

Table S193.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MKL1 MUTATED 1 8 0
MKL1 WILD-TYPE 60 77 22
'MKL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S194.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MKL1 MUTATED 2 3 2
MKL1 WILD-TYPE 40 44 62
'MKL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 1

Table S195.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MKL1 MUTATED 2 4 0 3
MKL1 WILD-TYPE 35 57 44 23
'MKL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.472 (Fisher's exact test), Q value = 1

Table S196.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MKL1 MUTATED 4 4 1
MKL1 WILD-TYPE 60 50 49
'MKL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S197.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MKL1 MUTATED 3 2 4
MKL1 WILD-TYPE 53 48 58
'MKL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S198.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MKL1 MUTATED 4 0 5
MKL1 WILD-TYPE 77 30 52
'MKL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S199.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MKL1 MUTATED 3 2 4
MKL1 WILD-TYPE 57 44 58
'MKL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.996 (Fisher's exact test), Q value = 1

Table S200.  Gene #25: 'MKL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MKL1 MUTATED 1 2 1 1 2 1 1
MKL1 WILD-TYPE 19 25 22 19 29 30 15
'MYH7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S201.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MYH7 MUTATED 3 2 1
MYH7 WILD-TYPE 58 83 21
'MYH7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S202.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MYH7 MUTATED 1 2 2
MYH7 WILD-TYPE 41 45 62
'MYH7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 1

Table S203.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MYH7 MUTATED 3 1 1 1
MYH7 WILD-TYPE 34 60 43 25
'MYH7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 1

Table S204.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MYH7 MUTATED 4 1 1
MYH7 WILD-TYPE 60 53 49
'MYH7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S205.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MYH7 MUTATED 3 1 2
MYH7 WILD-TYPE 53 49 60
'MYH7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0372 (Fisher's exact test), Q value = 1

Table S206.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MYH7 MUTATED 6 0 0
MYH7 WILD-TYPE 75 30 57

Figure S16.  Get High-res Image Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'MYH7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S207.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MYH7 MUTATED 2 1 3
MYH7 WILD-TYPE 58 45 59
'MYH7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 1

Table S208.  Gene #26: 'MYH7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MYH7 MUTATED 2 2 0 0 0 2 0
MYH7 WILD-TYPE 18 25 23 20 31 29 16
'MAP4K3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S209.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
MAP4K3 MUTATED 2 2 1
MAP4K3 WILD-TYPE 59 83 21
'MAP4K3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S210.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
MAP4K3 MUTATED 1 0 3
MAP4K3 WILD-TYPE 41 47 61
'MAP4K3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 1

Table S211.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
MAP4K3 MUTATED 0 1 3 1
MAP4K3 WILD-TYPE 37 60 41 25
'MAP4K3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 1

Table S212.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
MAP4K3 MUTATED 2 0 3
MAP4K3 WILD-TYPE 62 54 47
'MAP4K3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 1

Table S213.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
MAP4K3 MUTATED 2 3 0
MAP4K3 WILD-TYPE 54 47 62
'MAP4K3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S214.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
MAP4K3 MUTATED 4 1 0
MAP4K3 WILD-TYPE 77 29 57
'MAP4K3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 1

Table S215.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
MAP4K3 MUTATED 2 3 0
MAP4K3 WILD-TYPE 58 43 62
'MAP4K3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S216.  Gene #27: 'MAP4K3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
MAP4K3 MUTATED 1 1 1 0 0 2 0
MAP4K3 WILD-TYPE 19 26 22 20 31 29 16
'NEK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S217.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 61 85 22
NEK2 MUTATED 1 2 0
NEK2 WILD-TYPE 60 83 22
'NEK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S218.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 42 47 64
NEK2 MUTATED 0 1 2
NEK2 WILD-TYPE 42 46 62
'NEK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S219.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 37 61 44 26
NEK2 MUTATED 0 1 2 0
NEK2 WILD-TYPE 37 60 42 26
'NEK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 1

Table S220.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 54 50
NEK2 MUTATED 0 1 2
NEK2 WILD-TYPE 64 53 48
'NEK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 1

Table S221.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 50 62
NEK2 MUTATED 0 2 1
NEK2 WILD-TYPE 56 48 61
'NEK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S222.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 81 30 57
NEK2 MUTATED 0 1 2
NEK2 WILD-TYPE 81 29 55
'NEK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 1

Table S223.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 60 46 62
NEK2 MUTATED 0 2 1
NEK2 WILD-TYPE 60 44 61
'NEK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S224.  Gene #28: 'NEK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 27 23 20 31 31 16
NEK2 MUTATED 0 0 1 1 1 0 0
NEK2 WILD-TYPE 20 27 22 19 30 31 16
Methods & Data
Input
  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = KIRP-TP.transferedmergedcluster.txt

  • Number of patients = 168

  • Number of significantly mutated genes = 28

  • Number of Molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)